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--- readme.pedictf90 [2018/07/12 21:50] – created andres
+++ readme.pedictf90 [2020/03/13 18:51] – yutaka
@@ Line 2: / Line 2: @@
 This is program is used to do cross-validations. It reads a blupf90 parameter file, a solutions file
-and a data file
+and a data file.
 It needs ''OPTION include_effects'' followed by a series of effects.
 It computes
-y_hat = sum of estimates of the included effects
-y_star = y corrected by the other (not included) effects
+  * y_hat = sum of estimates of the included effects
-residual = y - included effects (not a true residual)
+  * y_star = y corrected by the other (not included) effects
+  * residual = y - included effects (not a true residual)
 For instance consider
-y = herd + age + animal + e
+  y = herd + age + animal + e
-with ''OPTION include_effects 3''
+with ''OPTION include_effects 3''.
-y_hat = animal_hat
+  * y_hat = animal_hat
-ystar = y - herd_hat - age_hat
+  * ystar = y - herd_hat - age_hat
-Which makes cor(y_hat,y_star) = cor(ebv, corrected y) which is a measure of accuracy
-it outputs the correlation between y_hat and y_star, for instance cor(ystar,yhat)=cor(u+e, uhat)
+Which makes cor(y_hat,y_star) = cor(ebv, corrected y) which is a measure of accuracy.
-and outputs these columns into a file, together with animal id (if there is animal in the model) or record number (if not)
+It outputs the correlation between y_hat and y_star, for instance cor(ystar,yhat)=cor(u+e, uhat) and outputs these columns into a file, together with animal id (if there is animal in the model) or record number (if not).
 In addition, if animal effect is in the model, it produces a file with ebvs from the solutions file.
+==== Output files ====
+=== yhat_residual ===
+The main file is ''yhat_residual'', which has corrected phenotypes and predicted residuals.
+The number of columns in this file depend on the number of traits (N).
+  * Column 1: Animal ID (renumbered i.e., same as the 1st column in renaddxx.ped)
+  * Column 2 to N+1: "y_star" explained above
+  * Column N+2 to 2N+1: "y_hat" explained above
+  * Column 2N+2 to 3N+1: "residual" explained above